Contacts of the strand formed by residues 11 - 19 (chain A) in PDB entry 3KG2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 11 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 1.3 72.6 - - - +
12A ILE* 1.3 62.0 + - - +
13A GLN* 3.7 4.4 + - - +
42A ARG* 3.7 5.2 - - - -
44A THR* 3.2 22.0 + - - +
71A TYR* 4.4 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 4.9 2.5 - - + +
11A SER* 1.3 73.7 + - - +
13A GLN* 1.3 61.5 + - - +
14A ILE* 3.6 14.2 + - + +
41A PHE* 3.9 25.4 - - + -
42A ARG 3.0 13.5 + - - +
43A LEU* 3.5 11.8 - - + -
44A THR* 2.9 24.3 + - - -
71A TYR* 3.7 31.4 - - + -
296A PHE* 3.6 34.8 - - + +
306A ILE* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.7 4.6 + - - +
12A ILE* 1.3 71.8 - - - +
14A ILE* 1.3 61.7 + - - +
44A THR* 3.5 18.4 - - + +
46A HIS* 6.6 0.2 - - + -
68A ARG 5.4 2.7 - - - +
69A GLY 4.3 15.5 - - - +
70A VAL* 3.4 8.0 - - + -
71A TYR* 3.0 38.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.1 18.4 - - + +
13A GLN* 1.3 80.5 - - - +
15A GLY* 1.3 64.5 + - - +
29A PHE* 4.6 18.6 - - + -
33A MET* 5.1 1.1 - - - -
43A LEU* 4.1 27.1 - - + -
44A THR 3.0 12.4 + - - +
45A PRO* 3.9 11.2 - - + -
46A HIS* 3.0 28.8 + - - +
70A VAL* 3.8 7.2 - - - +
72A ALA* 3.3 21.8 - - + +
74A PHE* 5.8 0.4 - - + -
292A MET* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 1.3 80.0 - - - +
16A GLY* 1.3 58.6 + - - -
17A LEU 4.2 0.2 - - - -
29A PHE* 5.7 1.3 - - - -
45A PRO* 5.7 0.7 - - - -
46A HIS* 4.0 6.3 - - - -
65A GLN* 4.6 11.0 - - - -
70A VAL* 3.8 10.8 - - - +
72A ALA 2.9 12.3 + - - -
73A ILE* 4.2 11.7 - - - -
74A PHE* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 1.3 73.5 - - - -
17A LEU* 1.3 65.2 + - - +
18A PHE* 3.6 19.5 + - - -
29A PHE* 5.5 2.9 - - - -
45A PRO* 6.1 0.4 - - - -
46A HIS 3.1 12.9 + - - +
47A ILE* 3.5 9.5 - - - -
48A ASP* 2.8 30.1 + - - +
74A PHE* 3.1 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 4.5 1.6 - - - -
16A GLY* 1.3 78.3 - - - +
18A PHE* 1.3 61.1 + - - +
19A PRO* 3.6 2.0 - - - +
48A ASP* 3.7 11.4 - - + +
58A VAL* 4.6 22.2 - - + +
61A ALA* 4.2 38.8 - - + +
62A PHE* 4.8 3.1 - - + +
65A GLN* 5.1 3.8 - - + -
73A ILE* 3.6 25.8 - - + -
74A PHE 2.8 9.1 + - - -
75A GLY* 3.1 25.6 - - - -
76A PHE* 3.3 19.1 + - - +
85A ILE* 4.6 12.1 - - + -
96A PHE* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 3.6 19.9 + - - -
17A LEU* 1.3 76.7 - - - +
19A PRO* 1.3 69.8 - - + +
22A ALA* 4.4 9.2 - - + +
25A GLU 4.0 7.2 - - - -
26A TYR* 3.7 49.6 - + + -
29A PHE* 3.4 22.4 - + + -
47A ILE* 4.1 12.3 - - + -
48A ASP 3.4 6.4 + - - -
49A ASN* 3.3 37.7 - - - +
50A LEU 3.6 2.6 + - - -
74A PHE* 3.3 39.0 - + - -
76A PHE* 3.9 13.9 - + - -
285A THR* 4.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.6 2.9 - - - +
18A PHE* 1.3 85.3 - - + +
20A ARG* 1.3 67.3 + - - +
22A ALA* 3.0 28.8 + - + +
49A ASN* 5.6 0.4 - - - -
50A LEU 3.4 11.4 - - - +
52A VAL* 3.7 37.0 - - + +
76A PHE* 3.4 35.7 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il